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Earth Mover's Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations.

Orlova DY, Zimmerman N, Meehan S, Meehan C, Waters J, Ghosn EE, Filatenkov A, Kolyagin GA, Gernez Y, Tsuda S, Moore W, Moss RB, Herzenberg LA, Walther G.

PLoS One. 2016 Mar 23;11(3):e0151859. doi: 10.1371/journal.pone.0151859.


A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732.


Rapid cytometric antibiotic susceptibility testing utilizing adaptive multidimensional statistical metrics.

Huang TH, Ning X, Wang X, Murthy N, Tzeng YL, Dickson RM.

Anal Chem. 2015 Feb 3;87(3):1941-9. doi: 10.1021/ac504241x.


Suppression of Foxo1 activity and down-modulation of CD62L (L-selectin) in HIV-1 infected resting CD4 T cells.

Trinité B, Chan CN, Lee CS, Mahajan S, Luo Y, Muesing MA, Folkvord JM, Pham M, Connick E, Levy DN.

PLoS One. 2014 Oct 16;9(10):e110719. doi: 10.1371/journal.pone.0110719.


Quantitative characterization of cellular membrane-receptor heterogeneity through statistical and computational modeling.

Weddell JC, Imoukhuede PI.

PLoS One. 2014 May 14;9(5):e97271. doi: 10.1371/journal.pone.0097271. Erratum in: PLoS One. 2014;9(8):e107095.


Flow cytometry bioinformatics.

O'Neill K, Aghaeepour N, Spidlen J, Brinkman R.

PLoS Comput Biol. 2013;9(12):e1003365. doi: 10.1371/journal.pcbi.1003365.


Soluble guanylate cyclase modulates alveolarization in the newborn lung.

Bachiller PR, Cornog KH, Kato R, Buys ES, Roberts JD Jr.

Am J Physiol Lung Cell Mol Physiol. 2013 Oct 15;305(8):L569-81. doi: 10.1152/ajplung.00401.2012.


Dengue virus activates membrane TRAIL relocalization and IFN-α production by human plasmacytoid dendritic cells in vitro and in vivo.

Gandini M, Gras C, Azeredo EL, Pinto LM, Smith N, Despres P, da Cunha RV, de Souza LJ, Kubelka CF, Herbeuval JP.

PLoS Negl Trop Dis. 2013 Jun 6;7(6):e2257. doi: 10.1371/journal.pntd.0002257.


Impact of viral attachment factor expression on antibody-mediated neutralization of flaviviruses.

Obara CJ, Dowd KA, Ledgerwood JE, Pierson TC.

Virology. 2013 Mar 1;437(1):20-7. doi: 10.1016/j.virol.2012.11.016.


Mapping and mining interictal pathological gamma (30-100 Hz) oscillations with clinical intracranial EEG in patients with epilepsy.

Smart O, Maus D, Marsh E, Dlugos D, Litt B, Meador K.

Expert Syst Appl. 2012 Jun 15;39(8):7355-7370.


DNA polymerase zeta is required for proliferation of normal mammalian cells.

Lange SS, Wittschieben JP, Wood RD.

Nucleic Acids Res. 2012 May;40(10):4473-82. doi: 10.1093/nar/gks054.


Astrocyte and macrophage regulation of YKL-40 expression and cellular response in neuroinflammation.

Bonneh-Barkay D, Bissel SJ, Kofler J, Starkey A, Wang G, Wiley CA.

Brain Pathol. 2012 Jul;22(4):530-46. doi: 10.1111/j.1750-3639.2011.00550.x.


FIND: a new software tool and development platform for enhanced multicolor flow analysis.

Dabdoub SM, Ray WC, Justice SS.

BMC Bioinformatics. 2011 May 10;12:145. doi: 10.1186/1471-2105-12-145.


Uracil DNA N-glycosylase promotes assembly of human centromere protein A.

Zeitlin SG, Chapados BR, Baker NM, Tai C, Slupphaug G, Wang JY.

PLoS One. 2011 Mar 2;6(3):e17151. doi: 10.1371/journal.pone.0017151.


Cell membrane modification for rapid display of bi-functional peptides: a novel approach to reduce complement activation.

Goga L, Perez-Abadia G, Pushpakumar SB, Cramer D, Yan J, Todnem N, Anderson G, Soni C, Barker J, Maldonado C.

Open Cardiovasc Med J. 2010 Jul 20;4:157-65. doi: 10.2174/1874192401004010157.


Data analysis in flow cytometry: the future just started.

Lugli E, Roederer M, Cossarizza A.

Cytometry A. 2010 Jul;77(7):705-13. doi: 10.1002/cyto.a.20901. Review.


Binding site on the transferrin receptor for the parvovirus capsid and effects of altered affinity on cell uptake and infection.

Goodman LB, Lyi SM, Johnson NC, Cifuente JO, Hafenstein SL, Parrish CR.

J Virol. 2010 May;84(10):4969-78. doi: 10.1128/JVI.02623-09.


flowClust: a Bioconductor package for automated gating of flow cytometry data.

Lo K, Hahne F, Brinkman RR, Gottardo R.

BMC Bioinformatics. 2009 May 14;10:145. doi: 10.1186/1471-2105-10-145.


STAT-3 and ERK 1/2 phosphorylation are critical for T-cell alloactivation and graft-versus-host disease.

Lu SX, Alpdogan O, Lin J, Balderas R, Campos-Gonzalez R, Wang X, Gao GJ, Suh D, King C, Chow M, Smith OM, Hubbard VM, Bautista JL, Cabrera-Perez J, Zakrzewski JL, Kochman AA, Chow A, Altan-Bonnet G, van den Brink MR.

Blood. 2008 Dec 15;112(13):5254-8. doi: 10.1182/blood-2008-03-147322.

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